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    SMAP1 small ArfGAP 1 [ Homo sapiens (human) ]

    Gene ID: 60682, updated on 27-Nov-2024

    Summary

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    Official Symbol
    SMAP1provided by HGNC
    Official Full Name
    small ArfGAP 1provided by HGNC
    Primary source
    HGNC:HGNC:19651
    See related
    Ensembl:ENSG00000112305 MIM:611372; AllianceGenome:HGNC:19651
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SMAP-1
    Summary
    The protein encoded by this gene is similar to the mouse stromal membrane-associated protein-1. This similarity suggests that this human gene product is also a type II membrane glycoprotein involved in the erythropoietic stimulatory activity of stromal cells. Alternate splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in brain (RPKM 17.8), esophagus (RPKM 10.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SMAP1 in Genome Data Viewer
    Location:
    6q13
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (70667883..70862015)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (71848459..72042553)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (71377586..71571718)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:71318535-71319052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:71319053-71319569 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:71326667-71326868 Neighboring gene spermine synthase pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24733 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17320 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17322 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17321 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:71386575-71387144 Neighboring gene solute carrier family 25 member 6 pseudogene 6 Neighboring gene transmembrane protein 192 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24734 Neighboring gene NADH:ubiquinone oxidoreductase subunit AB1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:71481211-71481711 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17323 Neighboring gene beta-1,3-glucuronyltransferase 2 Neighboring gene uncharacterized LOC105377850 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:71666023-71666538 Neighboring gene uncharacterized LOC124901229

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Cloning, characterization and chromosome mapping of the human SMAP1 gene. Marcos I, et al. Gene, 2002 Jun 12. PMID 12119110
    2. The Arf GTPase-activating protein SMAP1 promotes transferrin receptor endocytosis and interacts with SMAP2. Kobayashi N, et al. Biochem Biophys Res Commun, 2014 Oct 24. PMID 25281535
    3. Involvement of small ArfGAP1 (SMAP1), a novel Arf6-specific GTPase-activating protein, in microsatellite instability oncogenesis. Sangar F, et al. Oncogene, 2014 May 22. PMID 23752192
    4. Involvement of stromal membrane-associated protein (SMAP-1) in erythropoietic microenvironment. Sato Y, et al. J Biochem, 1998 Jul. PMID 9644265
    5. Mutation screening of three candidate genes, ELOVL5, SMAP1 and GLULD1 in autosomal recessive retinitis pigmentosa. Barragan I, et al. Int J Mol Med, 2005 Dec. PMID 16273301

    See all (47) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Pals1 functions in redundancy with SMAP1 to inhibit Arf6 in order to prevent Rac1-dependent colorectal cancer cell migration and invasion.
      Title: Pals1 functions in redundancy with SMAP1 to inhibit Arf6 in order to prevent Rac1-dependent colorectal cancer cell migration and invasion.
    2. The study identified a region on chromosome 6 comprising the genes SMAP1, B3GAT2, and RIMS1 as novel susceptibility locus for pediatric venous thromboembolism.
      Title: Rare genetic variants in SMAP1, B3GAT2, and RIMS1 contribute to pediatric venous thromboembolism.
    3. Results also demonstrated a physical association between SMAP1 and SMAP2, which might serve as a basis for a functional interaction, and identified the intramolecular domains responsible for this association
      Title: The Arf GTPase-activating protein SMAP1 promotes transferrin receptor endocytosis and interacts with SMAP2.
    4. SMAP1 loss-of-function mutations in microsatellite instability colorectal cancer may contribute to the emerging oncogenic pathway involving abnormal Arf6 regulation.
      Title: Involvement of small ArfGAP1 (SMAP1), a novel Arf6-specific GTPase-activating protein, in microsatellite instability oncogenesis.
    5. SMAP1 may be an ADP-ribosylation factor 6 (Arf6)GAP that specifically regulates one of the multiple functions of Arf6, namely, clathrin-dependent endocytosis
      Title: A novel GTPase-activating protein for ARF6 directly interacts with clathrin and regulates clathrin-dependent endocytosis.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of small ArfGAP 1 (SMAP1) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ13159, FLJ42245

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables clathrin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of erythrocyte differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of clathrin-dependent endocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    stromal membrane-associated protein 1
    Names
    stromal membrane-associated GTPase-activating protein 1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001044305.3 → NP_001037770.1  stromal membrane-associated protein 1 isoform A

      See identical proteins and their annotated locations for NP_001037770.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (A).
      Source sequence(s)
      AF442495, BC036123, DB480952
      Consensus CDS
      CCDS43478.1
      UniProtKB/Swiss-Prot
      Q53H70, Q5SYQ2, Q6PK24, Q8IYB5, Q8NDH4, Q96L38, Q96L39, Q9H8X4
      UniProtKB/TrEMBL
      A8K333
      Related
      ENSP00000359484.3, ENST00000370455.8
      Conserved Domains (1) summary
      pfam01412
      Location:20 → 120
      ArfGap; Putative GTPase activating protein for Arf

    2. NM_001281439.2 → NP_001268368.1  stromal membrane-associated protein 1 isoform C

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has multiple coding region differences, compared to variant 1, one of which results in a frameshift. The resulting protein (isoform C) has a distinct C-terminus and is shorter than isoform A.
      Source sequence(s)
      AF442495, AK023221, AL121961, BC008672, BC036123, DB480952
      Consensus CDS
      CCDS64459.1
      UniProtKB/TrEMBL
      B2RDK5
      Related
      ENSP00000359481.3, ENST00000370452.7
      Conserved Domains (1) summary
      pfam01412
      Location:20 → 120
      ArfGap; Putative GTPase activating protein for Arf

    3. NM_001281440.1 → NP_001268369.1  stromal membrane-associated protein 1 isoform D

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (D) has a distinct N-terminus and is shorter than isoform A.
      Source sequence(s)
      AF442495, AK307807, BC036123, DA527013
      Consensus CDS
      CCDS75478.1
      UniProtKB/TrEMBL
      A0A087X1X9, A8K333
      Related
      ENSP00000484538.1, ENST00000619054.4
      Conserved Domains (1) summary
      pfam01412
      Location:30 → 110
      ArfGap; Putative GTPase activating protein for Arf

    4. NM_021940.5 → NP_068759.2  stromal membrane-associated protein 1 isoform B

      See identical proteins and their annotated locations for NP_068759.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform B), compared to isoform A.
      Source sequence(s)
      AF442495, BC036123
      Consensus CDS
      CCDS4973.1
      UniProtKB/TrEMBL
      B2RDK5
      Related
      ENSP00000313382.5, ENST00000316999.9
      Conserved Domains (2) summary
      pfam01412
      Location:20 → 120
      ArfGap; Putative GTPase activating protein for Arf
      pfam09606
      Location:283 → 431
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      70667883..70862015
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011536047.4 → XP_011534349.1  stromal membrane-associated protein 1 isoform X6

      UniProtKB/TrEMBL
      B2RDK5
      Conserved Domains (1) summary
      pfam01412
      Location:20 → 120
      ArfGap; Putative GTPase activating protein for Arf

    2. XM_005248760.6 → XP_005248817.1  stromal membrane-associated protein 1 isoform X4

      Conserved Domains (1) summary
      pfam01412
      Location:20 → 120
      ArfGap; Putative GTPase activating protein for Arf

    3. XM_047419230.1 → XP_047275186.1  stromal membrane-associated protein 1 isoform X5

    4. XM_047419227.1 → XP_047275183.1  stromal membrane-associated protein 1 isoform X1

    5. XM_047419228.1 → XP_047275184.1  stromal membrane-associated protein 1 isoform X2

    6. XM_047419229.1 → XP_047275185.1  stromal membrane-associated protein 1 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      71848459..72042553
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356169.1 → XP_054212144.1  stromal membrane-associated protein 1 isoform X6

    2. XM_054356167.1 → XP_054212142.1  stromal membrane-associated protein 1 isoform X4

    3. XM_054356168.1 → XP_054212143.1  stromal membrane-associated protein 1 isoform X5

    4. XM_054356164.1 → XP_054212139.1  stromal membrane-associated protein 1 isoform X1

    5. XM_054356165.1 → XP_054212140.1  stromal membrane-associated protein 1 isoform X2

    6. XM_054356166.1 → XP_054212141.1  stromal membrane-associated protein 1 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IYB5.2 GenPept UniProtKB/Swiss-Prot:Q8IYB5

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